Yes they are two totally separate things and do not interact with each other…
The sync menu sends a program change according to what pattern your on using the channel set in the midi channels menu… It is relative to the pattern your on, for example pattern A1 would send pc 0, A2 would send pc 1, etc… This is most useful if you want to have another Elektron follow along so when you change from A1 to A2 on the digitakt, you other Elektron changes to A2 as well, it syncs the patterns…
The midi sequencer has a completely other program change feature that can send any bank and program change you want, to any channel using that tracks midi channel… Say you have a synth connected on channel 8 and want it to use its program number 33 or whatever when you use that midi track, it will do that… On another track you have a synth on channel 11 and want it to use its program 44 for that midi track, it can do that…
It’s possible to use them both at the same time as long as the program change in the sync menu is using a different channel… You can have an Elektron change to the same pattern number when you switch patterns on DT, and also have other synths changing their programs according to the midi tracks settings you made…
It’s very good that it behaves this way as it adds flexibility and is basically two different features…
I don’t have a DT, I’m an OT guy, but it’s pretty similar as are the workflow/settings for all Elektrons… What I don’t know is if you have your midi tracks muted if it will still send the change or not, or if you have to disable it on the midi track…
If you don’t need program change for anything just uncheck the boxes in the sync menu and don’t turn them on for the midi tracks… Just leave bank and prog set to off and don’t go messing with those settings…